A general ab initio approach for free energy landscapes of biological molecules around the transition states

Fusion of the classical molecular mechanics simulation and the quantum chemical calculation

Abstract

A general algorithm to obtain the free energy values at various molecular states was developed. The effectiveness of the algorithm was shown by the application to reveal the free energy landscape of the cis-trans imide isomerization of a peptide dimer, -Ala-Pro-, by performing the multicanonical molecular dynamics simulations and the ab initio molecular orbital calculations. Because of the generality of the current algorithm, many different kinds of applications are available for analyses of the free energies of biological molecules in the activated states.